Contacts of the helix formed by residues 29 - 39 (chain h) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 29 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23h GLU 4.8 1.5 + - - +
24h PHE* 3.5 20.7 - - + +
27h GLY 3.1 1.2 - - - -
28h PRO* 1.3 74.6 - - - +
30h SER* 1.3 52.7 + - - +
31h VAL* 3.0 6.1 - - - -
32h LEU* 2.7 32.0 + - + +
33h THR* 2.9 9.5 + - - -
60h ASP 6.1 1.3 - - - +
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Residues in contact with SER 30 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24h PHE 3.0 12.7 + - - -
25h ASN 3.1 27.6 - - - -
26h THR* 4.1 3.6 - - - -
27h GLY 3.0 17.7 + - - -
29h LEU* 1.3 75.7 - - - +
31h VAL* 1.3 53.8 + - - +
32h LEU 3.2 0.2 - - - -
33h THR* 3.7 5.4 - - - -
34h GLN* 2.7 36.0 + - - +
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Residues in contact with VAL 31 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28h PRO 3.2 15.5 + - - +
29h LEU* 3.0 0.4 - - - -
30h SER* 1.3 77.7 - - - +
32h LEU* 1.3 55.3 + - - +
34h GLN* 3.7 5.1 + - - +
35h SER* 3.2 25.6 + - - -
109h VAL* 5.4 5.8 - - + +
111h ARG* 5.1 20.0 - - + +
61i GLU 6.4 0.7 - - - -
62i VAL* 5.5 1.8 - - - -
63i LEU* 4.2 22.2 - - + +
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Residues in contact with LEU 32 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29h LEU* 2.7 20.5 + - + +
31h VAL* 1.3 71.6 - - - +
33h THR* 1.3 65.9 + - - +
35h SER* 3.1 7.5 + - - -
36h VAL* 3.0 25.5 + - - +
56h VAL* 4.8 3.1 - - - +
59h PHE* 4.3 24.0 - - + +
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Residues in contact with THR 33 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24h PHE* 3.5 31.4 - - - -
25h ASN* 4.7 5.6 - - - -
29h LEU 2.9 5.6 + - - -
30h SER* 3.8 7.0 - - - -
32h LEU* 1.3 77.7 - - - +
34h GLN* 1.3 59.0 + - - +
36h VAL* 3.6 4.5 + - - +
37h LYS* 3.2 23.2 + - - +
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Residues in contact with GLN 34 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30h SER 2.7 21.8 + - - +
31h VAL* 3.8 6.5 - - - +
33h THR* 1.3 73.2 - - - +
35h SER* 1.3 57.2 + - - +
37h LYS* 3.9 5.4 - - - +
38h ASN* 3.1 30.7 + - - +
40h THR* 5.3 0.5 - - - -
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Residues in contact with SER 35 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31h VAL 3.2 14.2 + - - -
32h LEU* 3.1 7.9 + - - -
34h GLN* 1.3 76.6 - - - +
36h VAL* 1.3 60.8 + - - +
39h ASN* 3.0 24.9 + - - -
40h THR* 3.1 31.5 + - - +
41h GLN 5.5 0.9 - - - -
42h VAL* 5.0 13.9 - - - -
56h VAL* 4.2 16.3 + - - +
111h ARG* 6.2 2.7 - - - -
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Residues in contact with VAL 36 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3449 ASN* 5.3 5.6 - - + -
3469 GLN* 5.5 9.9 - - + +
32h LEU 3.0 15.0 + - - +
33h THR* 4.1 4.7 - - - +
35h SER* 1.3 77.0 - - - +
37h LYS* 1.3 64.1 + - - +
39h ASN* 3.4 8.3 + - - +
56h VAL* 3.6 24.6 + - + +
57h LYS 4.7 9.4 - - - +
58h ALA* 5.4 2.9 - - - +
59h PHE 6.1 0.4 - - - +
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Residues in contact with LYS 37 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3469 GLN* 5.5 7.8 - - + +
33h THR 3.2 18.0 + - - +
34h GLN* 4.0 6.1 - - - +
35h SER 3.4 0.2 - - - -
36h VAL* 1.3 79.3 - - - +
38h ASN* 1.3 59.1 + - + +
39h ASN* 3.6 1.2 + - - +
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Residues in contact with ASN 38 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34h GLN 3.1 16.8 + - - +
37h LYS* 1.3 77.9 - - + +
39h ASN* 1.3 71.6 + - - +
40h THR* 3.3 13.3 + - - +
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Residues in contact with ASN 39 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35h SER 3.0 10.4 + - - -
36h VAL* 3.4 6.1 + - - +
37h LYS 3.3 4.0 - - - +
38h ASN* 1.3 80.2 - - - +
40h THR* 1.3 59.3 + - - +
55h ARG* 4.8 12.9 - - + +
56h VAL 5.6 2.5 - - - -
115h ILE* 5.2 1.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il